rs3768617

Variant names:

• chr1-183123365-C-T
• rs3768617
• NM_002293.4:c.2401+1114C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002293.4(LAMC1):​c.2401+1114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,840 control chromosomes in the GnomAD database, including 10,208 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (10208 hom., cov: 32)
• Consequence: LAMC1 NM_002293.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 26 publications found

Genes affected

LAMC1 (HGNC:6492): (laminin subunit gamma 1) Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins, composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively), have a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. Several isoforms of each chain have been described. Different alpha, beta and gamma chain isomers combine to give rise to different heterotrimeric laminin isoforms which are designated by Arabic numerals in the order of their discovery, i.e. alpha1beta1gamma1 heterotrimer is laminin 1. The biological functions of the different chains and trimer molecules are largely unknown, but some of the chains have been shown to differ with respect to their tissue distribution, presumably reflecting diverse functions in vivo. This gene encodes the gamma chain isoform laminin, gamma 1. The gamma 1 chain, formerly thought to be a beta chain, contains structural domains similar to beta chains, however, lacks the short alpha region separating domains I and II. The structural organization of this gene also suggested that it had diverged considerably from the beta chain genes. Embryos of transgenic mice in which both alleles of the gamma 1 chain gene were inactivated by homologous recombination, lacked basement membranes, indicating that laminin, gamma 1 chain is necessary for laminin heterotrimer assembly. It has been inferred by analogy with the strikingly similar 3' UTR sequence in mouse laminin gamma 1 cDNA, that multiple polyadenylation sites are utilized in human to generate the 2 different sized mRNAs (5.5 and 7.5 kb) seen on Northern analysis. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAMC1	NM_002293.4	c.2401+1114C>T		intron_variant	Intron 13 of 27	ENST00000258341.5	NP_002284.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAMC1	ENST00000258341.5	c.2401+1114C>T		intron_variant	Intron 13 of 27	1	NM_002293.4	ENSP00000258341.3

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51703 AN: 151722 Hom.: 10200 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.371

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.341 AC: 51724 AN: 151840 Hom.: 10208 Cov.: 32 AF XY: 0.346 AC XY: 25641 AN XY: 74186

African (AFR) AF: 0.128 AC: 5316 AN: 41502

American (AMR) AF: 0.372 AC: 5665 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1373 AN: 3462

East Asian (EAS) AF: 0.482 AC: 2481 AN: 5148

South Asian (SAS) AF: 0.382 AC: 1836 AN: 4808

European-Finnish (FIN) AF: 0.494 AC: 5180 AN: 10496

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28482 AN: 67884

Other (OTH) AF: 0.376 AC: 792 AN: 2108

Alfa AF: 0.392 Hom.: 8780

Bravo AF: 0.321

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.48
PhyloP100		-0.061
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3768617; hg19: chr1-183092500;